Gel retardation or electrophoretic mobility shift assay (EMSA) is a useful method for visualizing specific interactions between DNA-binding proteins and DNA. DNA-binding proteins are involved in a variety of cellular processes ranging from transcription and replication to recombination and viral integration. Typically, .sup.32 P-labeled DNA probes containing the sequence bound by the protein of interest are used in mobility shift assays, but a non-radioactive method using DNA labeled with digoxygenin-dUTP has previously been described (Suske et al., 1989, Nucleic Acids Res. 17:4405). While hybridization of non-radioactive labeled probes has been employed in Southern or Northern analysis, and other than the method described by Suske et al., use of non-radioactive labeled probes directly for studying protein-polynucleotide interactions with EMSA has not previously been described.